bionemo_infra

Tools maintained by the BioNeMo Framework Infrastructure team.

Development

All code must be formatted & linted using ruff and type checked using mypy.

To type check, run:

mypy --install-types --non-interactive --ignore-missing --check-untyped-defs .

All code must have type annotations. In special circumstances, such as private or helper functions, may elide static
type annotations if it is beneficial.

To run unit tests, use pytest -v. Unit tests must cover all features and known bug cases.

To get code coverage reports, run:

pytest -v --cov=infra_bionemo --cov-report=term --cov-report=html .

Then, open the HTML coverage report in your browser. Note that file coverage stats are reported
in the terminal too.

First Time Setup

For first time setup, be sure to install the development and test dependencies of the entire bionemo repository.
These are defined at the repository's top-level pyproject.toml file. Follow the instructions
outlined in the top-level README. Once you have your local virtual environment ready, you may
install this project's code by running the following:

uv pip install --editable .

NOTE: you may have to re-install the project if there are new or removed packages. If the requirements haven't changed,
you can re-install without re-installing the dependencies by doing: uv pip install --no-deps -e .

Versioning

This project uses Semantic Versioning 2.0. Contributors MUST update the version in
pyproject.toml correctly in their MRs. The CI will reject MRs that do not increment the version number correctly.